Sharegate does not automatically copy groups and permission levels because this could result in undesired behavior depending on the scenario.
There are 3 circumstances in which Sharegate will copy those objects:
- They are migrated directly (not yet possible in PowerShell)
- The migration is from and to a top level site (not subsite)
- The permission level does not exist at the destination and it is a dependence to an object that is copied. For instance: Site A has some custom permissions and John has a 'Custom Read' on Site A. When Site A is migrated, 'Custom Read' will be migrated to the destination as well.